# Package picard.sam.markduplicates.util

package picard.sam.markduplicates.util

Related Packages
Package
Description
picard.sam.markduplicates
Class
Description
AbstractMarkDuplicatesCommandLineProgram
Abstract class that holds parameters and methods common to classes that perform duplicate detection and/or marking within SAM/BAM/CRAM files.
AbstractMarkDuplicatesCommandLineProgram.SamHeaderAndIterator
Little class used to package up a header and an iterable/iterator.
AbstractOpticalDuplicateFinderCommandLineProgram
Abstract class that holds parameters and methods common to classes that optical duplicate detection.
DiskBasedReadEndsForMarkDuplicatesMap
Disk-based implementation of ReadEndsForMarkDuplicatesMap.
LibraryIdGenerator
A class to generate library Ids and keep duplication metrics by library IDs.
MarkQueue
This is the mark queue.
MemoryBasedReadEndsForMarkDuplicatesMap
Map from String to ReadEnds object.
OpticalDuplicateFinder
Contains methods for finding optical/co-localized/sequencing duplicates.
PhysicalLocationForMateCigar
Stores the minimal information needed for optical duplicate detection.
PhysicalLocationForMateCigarSet
This stores records that are comparable for detecting optical duplicates.
ReadEnds
Little struct-like class to hold read pair (and fragment) end data for duplicate marking.
ReadEndsForMarkDuplicates
Little struct-like class to hold read pair (and fragment) end data for MarkDuplicatesWithMateCigar
ReadEndsForMarkDuplicatesCodec
Codec for ReadEnds that just outputs the primitive fields and reads them back.
ReadEndsForMarkDuplicatesMap
Interface for storing and retrieving ReadEnds objects.
ReadEndsForMarkDuplicatesWithBarcodes
ReadEndsForMarkDuplicatesWithBarcodesCodec
Created by nhomer on 9/13/15.
ReadEndsForMateCigar
A class to store individual records for MarkDuplicatesWithMateCigar.
RepresentativeReadIndexerCodec
Codec for read names and integers that outputs the primitive fields and reads them back.
SamRecordWithOrdinalAndSetDuplicateReadFlag
This class sets the duplicate read flag as the result state when examining sets of records.